# Documentation for Gating-ML.v2.0

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Logical Diagram:
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XML Instance Representation:
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Diagram:
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Schema Component Representation:
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## Table of Contents

- Schema Document Properties
- Global Definitions
  - Complex Type: AbstractTransformation_Type
  - Complex Type: FASinHTransformation_Type
  - Complex Type: FCSDimensions_Type
  - Complex Type: FLinTransformation_Type
  - Complex Type: FLogTransformation_Type
  - Complex Type: FRatioTransformation_Type
  - Complex Type: HyperlogTransformation_Type
  - Complex Type: LogicleTransformation_Type
  - Complex Type: SpectrumCoefficient_Type
  - Complex Type: SpectrumMatrix_Type
  - Complex Type: Spectrum_Type
  - Complex Type: transformation_Type
  - Model Group: SpectrumMatrix_Group
  - Model Group: Transformation_Group

- Legend

- Glossary

#### Master schema documentation file: Gating-ML.v2.0.xsd.html

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## Schema Document Properties

Target Namespace | http://www.isac-net.org/std/Gating-ML/v2.0/transformations
Version | 2.0.121207
Element and Attribute Namespaces | Global element and attribute declarations belong to this schema's target namespace. By default, local element declarations belong to this schema's target namespace. By default, local attribute declarations belong to this schema's target namespace.
Schema Composition | This schema imports schema(s) from the following namespace(s): http://www.isac-net.org/std/Gating-ML/v2.0/datatypes (at DataTypes.v2.0.xsd)
Documentation | Josef Spidlen jspidlen@bccrc.ca Copyright (c) 2008-2012 ISAC (International Society for Advancement of Cytometry) Free of charge distribution and read-only usage permited. Modification and all other rights reserved. For all other uses please contact ISAC.
Application Data | Transformation descriptions within Gating-ML. More information at: http://flowcyt.sourceforge.net/.

### Declared Namespaces

Prefix | Namespace
--- | ---
Default namespace | http://www.w3.org/2001/XMLSchema
data-type | http://www.isac-net.org/std/Gating-ML/v2.0/datatypes
xml | http://www.w3.org/XML/1998/namespace
mml | http://www.w3.org/1998/Math/MathML
transforms | http://www.isac-net.org/std/Gating-ML/v2.0/transformations

Schema Component Representation
<schema targetNamespace="http://www.isac-net.org/std/Gating-ML/v2.0/transformations" elementFormDefault="qualified" attributeFormDefault="qualified" version="2.0.121207">
<import namespace="http://www.isac-net.org/std/Gating-ML/v2.0/datatypes" schemaLocation="DataTypes.v2.0.xsd"/>
...
</schema>
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## Global Definitions

### Complex Type: AbstractTransformation_Type

Super-types: | None
Sub-types: | FLinTransformation_Type (by extension) FRatioTransformation_Type (by extension) FLogTransformation_Type (by extension) FASinHTransformation_Type (by extension) HyperlogTransformation_Type (by extension) LogicleTransformation_Type (by extension) SpectrumMatrix_Type (by extension)

Name | AbstractTransformation_Type
Abstract | yes
Documentation | Abstract type to be used as a common parent of all transformations.

XML Instance Representation
<...>
Start Group: data-type:Custom_Group [0..1]
Start Choice [1]
<data-type:custom_info> anyType </data-type:custom_info> [1]
End Choice
End Group: data-type:Custom_Group
</...>
Diagram
Schema Component Representation
<complexType name="AbstractTransformation_Type" abstract="true">
<group ref=" data-type:Custom_Group " minOccurs="0"/>
</complexType>
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### Complex Type: FASinHTransformation_Type

Super-types: | AbstractTransformation_Type < FASinHTransformation_Type (by extension)
Sub-types: | None

Name | FASinHTransformation_Type
Abstract | no

XML Instance Representation
<...
transforms:T=" data-type:PFloat64_Type [1]"
transforms:M=" data-type:PFloat64_Type [1]"
transforms:A=" data-type:UFloat64_Type [1]">
Start Group: data-type:Custom_Group [0..1]
Start Choice [1]
<data-type:custom_info> anyType </data-type:custom_info> [1]
End Choice
End Group: data-type:Custom_Group
</...>
Diagram
Schema Component Representation
<complexType name="FASinHTransformation_Type">
<complexContent>
<extension base=" transforms:AbstractTransformation_Type ">
<attribute name="T" type=" data-type:PFloat64_Type " use="required"/>
<attribute name="M" type=" data-type:PFloat64_Type " use="required"/>
<attribute name="A" type=" data-type:UFloat64_Type " use="required"/>
</extension>
<-- XSD1.1 allows us to place the following assertion stating that T>A <assert test="@M gte @A" /> However, we have found experimentally that this test fails at the XML instance level even even if this condition is met. Curently, the cause of this problem is unclear, which lead us to commenting out the assetion and leaving it up to the implementing software to verify that attribute values are correct. -->
</complexContent>
</complexType>
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### Complex Type: FCSDimensions_Type

Super-types: | None
Sub-types: | None

Name | FCSDimensions_Type
Abstract | no

XML Instance Representation
<...>
Start Group: data-type:FCSDimensions_Group [2..*]
<data-type:fcs-dimension> data-type:NonEmptyName_Type </data-type:fcs-dimension> [1]
End Group: data-type:FCSDimensions_Group
</...>
Diagram
Schema Component Representation
<complexType name="FCSDimensions_Type">
<group ref=" data-type:FCSDimensions_Group " minOccurs="2" maxOccurs="unbounded"/>
</complexType>
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### Complex Type: FLinTransformation_Type

Super-types: | AbstractTransformation_Type < FLinTransformation_Type (by extension)
Sub-types: | None

Name | FLinTransformation_Type
Abstract | no

XML Instance Representation
<...
transforms:A=" data-type:Float64_Type [1]"
transforms:T=" data-type:PFloat64_Type [1]">
Start Group: data-type:Custom_Group [0..1]
Start Choice [1]
<data-type:custom_info> anyType </data-type:custom_info> [1]
End Choice
End Group: data-type:Custom_Group
</...>
Diagram
Schema Component Representation
<complexType name="FLinTransformation_Type">
<complexContent>
<extension base=" transforms:AbstractTransformation_Type ">
<attribute name="A" type=" data-type:Float64_Type " use="required"/>
<attribute name="T" type=" data-type:PFloat64_Type " use="required"/>
<-- XSD1.1 allows us to place the following assertion stating that T>A <assert test="@T gte @A" /> However, we have found experimentally that this test fails at the XML instance level even even if this condition is met. Curently, the cause of this problem is unclear, which lead us to commenting out the assetion and leaving it up to the implementing software to verify that attribute values are correct. -->
</extension>
</complexContent>
</complexType>
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### Complex Type: FLogTransformation_Type

Super-types: | AbstractTransformation_Type < FLogTransformation_Type (by extension)
Sub-types: | None

Name | FLogTransformation_Type
Abstract | no

XML Instance Representation
<...
transforms:T=" data-type:PFloat64_Type [1]"
transforms:M=" data-type:PFloat64_Type [1]">
Start Group: data-type:Custom_Group [0..1]
Start Choice [1]
<data-type:custom_info> anyType </data-type:custom_info> [1]
End Choice
End Group: data-type:Custom_Group
</...>
Diagram
Schema Component Representation
<complexType name="FLogTransformation_Type">
<complexContent>
<extension base=" transforms:AbstractTransformation_Type ">
<attribute name="T" type=" data-type:PFloat64_Type " use="required"/>
<attribute name="M" type=" data-type:PFloat64_Type " use="required"/>
</extension>
</complexContent>
</complexType>
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### Complex Type: FRatioTransformation_Type

Super-types: | AbstractTransformation_Type < FRatioTransformation_Type (by extension)
Sub-types: | None

Name | FRatioTransformation_Type
Abstract | no

XML Instance Representation
<...
transforms:A=" data-type:Float64_Type [1]"
transforms:B=" data-type:Float64_Type [1]"
transforms:C=" data-type:Float64_Type [1]">
Start Group: data-type:Custom_Group [0..1]
Start Choice [1]
<data-type:custom_info> anyType </data-type:custom_info> [1]
End Choice
End Group: data-type:Custom_Group
Start Group: data-type:FCSDimensions_Group [2..2]
<data-type:fcs-dimension> data-type:NonEmptyName_Type </data-type:fcs-dimension> [1]
End Group: data-type:FCSDimensions_Group
</...>
Diagram
Schema Component Representation
<complexType name="FRatioTransformation_Type">
<complexContent>
<extension base=" transforms:AbstractTransformation_Type ">
<group ref=" data-type:FCSDimensions_Group " minOccurs="2" maxOccurs="2"/>
<attribute name="A" type=" data-type:Float64_Type " use="required"/>
<attribute name="B" type=" data-type:Float64_Type " use="required"/>
<attribute name="C" type=" data-type:Float64_Type " use="required"/>
</extension>
</complexContent>
</complexType>
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### Complex Type: HyperlogTransformation_Type

Super-types: | AbstractTransformation_Type < HyperlogTransformation_Type (by extension)
Sub-types: | None

Name | HyperlogTransformation_Type
Abstract | no

XML Instance Representation
<...
transforms:T=" data-type:PFloat64_Type [1]"
transforms:M=" data-type:PFloat64_Type [1]"
transforms:W=" data-type:PFloat64_Type [1]"
transforms:A=" data-type:Float64_Type [1]">
Start Group: data-type:Custom_Group [0..1]
Start Choice [1]
<data-type:custom_info> anyType </data-type:custom_info> [1]
End Choice
End Group: data-type:Custom_Group
</...>
Diagram
Schema Component Representation
<complexType name="HyperlogTransformation_Type">
<complexContent>
<extension base=" transforms:AbstractTransformation_Type ">
<attribute name="T" type=" data-type:PFloat64_Type " use="required"/>
<attribute name="M" type=" data-type:PFloat64_Type " use="required"/>
<attribute name="W" type=" data-type:PFloat64_Type " use="required"/>
<attribute name="A" type=" data-type:Float64_Type " use="required"/>
<-- XSD1.1 allows us to place the following assertions stating that W >= M/2, -W <= A <= M-2W <assert test="@W le ((@M) div 2)" /> <assert test="@A ge ((-1)*(@W))" /> <assert test="@A le (@M)-(2*@W)"/> However, we have found experimentally that these tests fails at the XML instance level even even if these conditions are met. Curently, the cause of this problem is unclear, which lead us to commenting out the assetion and leaving it up to the implementing software to verify that attribute values are correct. -->
</extension>
</complexContent>
</complexType>
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### Complex Type: LogicleTransformation_Type

Super-types: | AbstractTransformation_Type < LogicleTransformation_Type (by extension)
Sub-types: | None

Name | LogicleTransformation_Type
Abstract | no

XML Instance Representation
<...
transforms:T=" data-type:PFloat64_Type [1]"
transforms:M=" data-type:PFloat64_Type [1]"
transforms:W=" data-type:UFloat64_Type [1]"
transforms:A=" data-type:Float64_Type [1]">
Start Group: data-type:Custom_Group [0..1]
Start Choice [1]
<data-type:custom_info> anyType </data-type:custom_info> [1]
End Choice
End Group: data-type:Custom_Group
</...>
Diagram
Schema Component Representation
<complexType name="LogicleTransformation_Type">
<complexContent>
<extension base=" transforms:AbstractTransformation_Type ">
<attribute name="T" type=" data-type:PFloat64_Type " use="required"/>
<attribute name="M" type=" data-type:PFloat64_Type " use="required"/>
<attribute name="W" type=" data-type:UFloat64_Type " use="required"/>
<attribute name="A" type=" data-type:Float64_Type " use="required"/>
<-- XSD1.1 allows us to place the following assertions stating that W >= M/2, -W <= A <= M-2W <assert test="@W le ((@M) div 2)" /> <assert test="@A ge ((-1)*(@W))" /> <assert test="@A le (@M)-(2*@W)"/> However, we have found experimentally that these tests fails at the XML instance level even even if these conditions are met. Curently, the cause of this problem is unclear, which lead us to commenting out the assetion and leaving it up to the implementing software to verify that attribute values are correct. -->
</extension>
</complexContent>
</complexType>
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### Complex Type: SpectrumCoefficient_Type

Super-types: | None
Sub-types: | None

Name | SpectrumCoefficient_Type
Abstract | no

XML Instance Representation
<...
transforms:value=" data-type:Float64_Type [1]"/>
Diagram
Schema Component Representation
<complexType name="SpectrumCoefficient_Type">
<attribute name="value" type=" data-type:Float64_Type " use="required"/>
</complexType>
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### Complex Type: SpectrumMatrix_Type

Super-types: | AbstractTransformation_Type < SpectrumMatrix_Type (by extension)
Sub-types: | None

Name | SpectrumMatrix_Type
Abstract | no

XML Instance Representation
<...
transforms:id="ID [1]"
transforms:matrix-inverted-already="boolean [0..1]">
Start Group: data-type:Custom_Group [0..1]
Start Choice [1]
<data-type:custom_info> anyType </data-type:custom_info> [1]
End Choice
End Group: data-type:Custom_Group
<transforms:fluorochromes> transforms:FCSDimensions_Type </transforms:fluorochromes> [1]
<transforms:detectors> transforms:FCSDimensions_Type </transforms:detectors> [1]
<transforms:spectrum> transforms:Spectrum_Type </transforms:spectrum> [1..*]
</...>
Diagram
Schema Component Representation
<complexType name="SpectrumMatrix_Type">
<complexContent>
<extension base=" transforms:AbstractTransformation_Type ">
<sequence>
<element name="fluorochromes" type=" transforms:FCSDimensions_Type "/>
<element name="detectors" type=" transforms:FCSDimensions_Type "/>
<element name="spectrum" type=" transforms:Spectrum_Type " minOccurs="1" maxOccurs="unbounded"/>
</sequence>
<attribute name="id" type=" ID " use="required"/>
<attribute name="matrix-inverted-already" type=" boolean " default="false" use="optional" id="matrix-inverted-already"/>
</extension>
</complexContent>
</complexType>
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### Complex Type: Spectrum_Type

Super-types: | None
Sub-types: | None

Name | Spectrum_Type
Abstract | no
Documentation | Row of the spillover/spectrum matrix.

XML Instance Representation
<...>
<transforms:coefficient> transforms:SpectrumCoefficient_Type </transforms:coefficient> [1..*]
</...>
Diagram
Schema Component Representation
<complexType name="Spectrum_Type">
<sequence>
<element name="coefficient" type=" transforms:SpectrumCoefficient_Type " minOccurs="1" maxOccurs="unbounded"/>
</sequence>
</complexType>
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### Complex Type: transformation_Type

Super-types: | None
Sub-types: | None

Name | transformation_Type
Abstract | no
Documentation | Transformations are functions applicable on one or more FCS dimensions; they receive an id attribute to be referencable from gating descriptions.

XML Instance Representation
<...
transforms:id="ID [1]">
Start Choice [1]
<transforms:flin> transforms:FLinTransformation_Type </transforms:flin> [1]
<transforms:fratio> transforms:FRatioTransformation_Type </transforms:fratio> [1]
<transforms:flog> transforms:FLogTransformation_Type </transforms:flog> [1]
<transforms:fasinh> transforms:FASinHTransformation_Type </transforms:fasinh> [1]
<transforms:hyperlog> transforms:HyperlogTransformation_Type </transforms:hyperlog> [1]
<transforms:logicle> transforms:LogicleTransformation_Type </transforms:logicle> [1]
End Choice
</...>
Diagram
Schema Component Representation
<complexType name="transformation_Type">
<sequence>
<choice>
<element name="flin" type=" transforms:FLinTransformation_Type " id="flin"/>
<element name="fratio" type=" transforms:FRatioTransformation_Type " id="fratio"/>
<element name="flog" type=" transforms:FLogTransformation_Type " id="flog"/>
<element name="fasinh" type=" transforms:FASinHTransformation_Type " id="asinh"/>
<element name="hyperlog" type=" transforms:HyperlogTransformation_Type " id="hyperlog"/>
<element name="logicle" type=" transforms:LogicleTransformation_Type " id="logicle"/>
</choice>
</sequence>
<attribute name="id" type=" ID " use="required"/>
</complexType>
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### Model Group: SpectrumMatrix_Group

Name | SpectrumMatrix_Group

XML Instance Representation
Start Choice [1]
<transforms:spectrumMatrix> transforms:SpectrumMatrix_Type </transforms:spectrumMatrix> [1]
End Choice
Diagram
Schema Component Representation
<group name="SpectrumMatrix_Group">
<choice>
<element name="spectrumMatrix" type=" transforms:SpectrumMatrix_Type "/>
</choice>
</group>
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### Model Group: Transformation_Group

Name | Transformation_Group

XML Instance Representation
Start Choice [1]
<transforms:transformation> transforms:transformation_Type </transforms:transformation> [1]
End Choice
Diagram
Schema Component Representation
<group name="Transformation_Group">
<choice>
<element name="transformation" type=" transforms:transformation_Type " id="transformation"/>
</choice>
</group>
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## Legend

### Complex Type:

Schema Component Type

### AusAddress

Schema Component Name

Super-types: | Address < AusAddress (by extension)
Sub-types: | QLDAddress (by restriction)

If this schema component is a type definition, its type hierarchy is shown in a gray-bordered box.

Name | AusAddress
Abstract | no

The table above displays the properties of this schema component.
XML Instance Representation
<... country="Australia" >
<unitNo> string </unitNo> [0..1]
<houseNo> string </houseNo> [1]
<street> string </street> [1]
Start Choice [1]
<city> string </city> [1]
<town> string </town> [1]
End Choice
<state> AusStates </state> [1]
<postcode> string <<pattern = [1-9][0-9]{3}>> </postcode> [1] ?
</...>

The XML Instance Representation table above shows the schema component's content as an XML instance.

- The minimum and maximum occurrence of elements and attributes are provided in square brackets, e.g. [0..1].
- Model group information are shown in gray, e.g. Start Choice ... End Choice.
- For type derivations, the elements and attributes that have been added to or changed from the base type's content are shown in bold.
- If an element/attribute has a fixed value, the fixed value is shown in green, e.g. country="Australia".
- Otherwise, the type of the element/attribute is displayed.
  - If the element/attribute's type is in the schema, a link is provided to it.
  - For local simple type definitions, the constraints are displayed in angle brackets, e.g. <<pattern = [1-9][0-9]{3}>>.
- If a local element/attribute has documentation, it will be displayed in a window that pops up when the question mark inside the attribute or next to the element is clicked, e.g. <postcode>.

Schema Component Representation
<complexType name="AusAddress">
<complexContent>
<extension base=" Address ">
<sequence>
<element name="state" type=" AusStates "/>
<element name="postcode">
<simpleType>
<restriction base=" string ">
<pattern value="[1-9][0-9]{3}"/>
</restriction>
</simpleType>
</element>
</sequence>
<attribute name="country" type=" string " fixed="Australia"/>
</extension>
</complexContent>
</complexType>
The Schema Component Representation table above displays the underlying XML representation of the schema component. (Annotations are not shown.)
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## Glossary

Abstract (Applies to complex type definitions and element declarations). An abstract element or complex type cannot used to validate an element instance. If there is a reference to an abstract element, only element declarations that can substitute the abstract element can be used to validate the instance. For references to abstract type definitions, only derived types can be used.

All Model Group Child elements can be provided in any order in instances. See: http://www.w3.org/TR/xmlschema-1/#element-all.

Choice Model Group Only one from the list of child elements and model groups can be provided in instances. See: http://www.w3.org/TR/xmlschema-1/#element-choice.

Collapse Whitespace Policy Replace tab, line feed, and carriage return characters with space character (Unicode character 32). Then, collapse contiguous sequences of space characters into single space character, and remove leading and trailing space characters.

Disallowed Substitutions (Applies to element declarations). If substitution is specified, then substitution group members cannot be used in place of the given element declaration to validate element instances. If derivation methods, e.g. extension, restriction, are specified, then the given element declaration will not validate element instances that have types derived from the element declaration's type using the specified derivation methods. Normally, element instances can override their declaration's type by specifying an `xsi:type` attribute.

Key Constraint Like Uniqueness Constraint, but additionally requires that the specified value(s) must be provided. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

Key Reference Constraint Ensures that the specified value(s) must match value(s) from a Key Constraint or Uniqueness Constraint. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

Model Group Groups together element content, specifying the order in which the element content can occur and the number of times the group of element content may be repeated. See: http://www.w3.org/TR/xmlschema-1/#Model_Groups.

Nillable (Applies to element declarations). If an element declaration is nillable, instances can use the `xsi:nil` attribute. The `xsi:nil` attribute is the boolean attribute, nil, from the http://www.w3.org/2001/XMLSchema-instance namespace. If an element instance has an `xsi:nil` attribute set to true, it can be left empty, even though its element declaration may have required content.

Notation A notation is used to identify the format of a piece of data. Values of elements and attributes that are of type, NOTATION, must come from the names of declared notations. See: http://www.w3.org/TR/xmlschema-1/#cNotation_Declarations.

Preserve Whitespace Policy Preserve whitespaces exactly as they appear in instances.

Prohibited Derivations (Applies to type definitions). Derivation methods that cannot be used to create sub-types from a given type definition.

Prohibited Substitutions (Applies to complex type definitions). Prevents sub-types that have been derived using the specified derivation methods from validating element instances in place of the given type definition.

Replace Whitespace Policy Replace tab, line feed, and carriage return characters with space character (Unicode character 32).

Sequence Model Group Child elements and model groups must be provided in the specified order in instances. See: http://www.w3.org/TR/xmlschema-1/#element-sequence.

Substitution Group Elements that are members of a substitution group can be used wherever the head element of the substitution group is referenced.

Substitution Group Exclusions (Applies to element declarations). Prohibits element declarations from nominating themselves as being able to substitute a given element declaration, if they have types that are derived from the original element's type using the specified derivation methods.

Target Namespace The target namespace identifies the namespace that components in this schema belongs to. If no target namespace is provided, then the schema components do not belong to any namespace.

Uniqueness Constraint Ensures uniqueness of an element/attribute value, or a combination of values, within a specified scope. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

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